Variant report

Variant	rs4299940
Chromosome Location	chr7:99793942-99793943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr7:99793349-99794068	GM12878	blood:	n/a	n/a
2	EP300	chr7:99793620-99793984	GM12878	blood:	n/a	chr7:99793808-99793822
3	PAX5	chr7:99793906-99794237	GM12878	blood:	n/a	n/a
4	PML	chr7:99793552-99794125	GM12878	blood:	n/a	n/a
5	BCL11A	chr7:99793731-99793986	GM12878	blood:	n/a	chr7:99793808-99793817
6	PAX5	chr7:99793807-99794192	GM12878	blood:	n/a	chr7:99793808-99793817
7	SPI1	chr7:99793607-99794022	GM12891	blood:	n/a	n/a
8	POLR2A	chr7:99793922-99794263	GM12878	blood:	n/a	n/a
9	NFATC1	chr7:99793576-99794019	GM12878	blood:	n/a	n/a
10	ZNF384	chr7:99793600-99794096	GM12878	blood:	n/a	n/a
11	SPI1	chr7:99793410-99794321	GM12878	blood:	n/a	n/a
12	EBF1	chr7:99793916-99794194	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:99793821-99795067	K562	blood:	n/a	n/a
14	STAT5A	chr7:99793657-99794015	GM12878	blood:	n/a	chr7:99793806-99793817
15	SPI1	chr7:99793615-99793972	GM12878	blood:	n/a	n/a
16	BCLAF1	chr7:99793577-99794076	GM12878	blood:	n/a	chr7:99793808-99793817
17	BHLHE40	chr7:99793775-99793997	GM12878	blood:	n/a	n/a
18	POU2F2	chr7:99793684-99794185	GM12878	blood:	n/a	n/a
19	RUNX3	chr7:99793475-99794060	GM12878	blood:	n/a	n/a
20	NFIC	chr7:99793574-99794114	GM12878	blood:	n/a	n/a
21	SPI1	chr7:99793683-99794077	GM12891	blood:	n/a	n/a
22	FOXM1	chr7:99793622-99794058	GM12878	blood:	n/a	n/a
23	MTA3	chr7:99793596-99794126	GM12878	blood:	n/a	n/a
24	EBF1	chr7:99793782-99793982	GM12878	blood:	n/a	n/a
25	RUNX3	chr7:99793211-99794076	GM12878	blood:	n/a	n/a
26	EP300	chr7:99793690-99793954	GM12878	blood:	n/a	chr7:99793808-99793822
27	IRF4	chr7:99793570-99794053	GM12878	blood:	n/a	n/a
28	ATF2	chr7:99793579-99794110	GM12878	blood:	n/a	n/a
29	ATF2	chr7:99793594-99794068	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99791489..99794024-chr7:99807798..99809792,2	K562	blood:

Variant related genes	Relation type
STAG3	TF binding region
ENSG00000239521	Chromatin interaction
ENSG00000066923	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1043915	0.83[AFR][1000 genomes]
rs10953295	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11764176	0.85[AFR][1000 genomes]
rs11767968	0.85[AFR][1000 genomes]
rs12705073	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13230744	0.82[AFR][1000 genomes]
rs1624099	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727128	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727129	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727143	0.81[EUR][1000 genomes]
rs1727145	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859787	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246713	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272344	0.85[AFR][1000 genomes]
rs2906646	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2950518	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3735241	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3735242	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3779046	0.83[AFR][1000 genomes]
rs4729579	0.83[AFR][1000 genomes]
rs4729580	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55796551	0.83[AFR][1000 genomes]
rs6465764	0.83[AFR][1000 genomes]
rs6465766	0.85[AFR][1000 genomes]
rs66809776	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6948729	0.85[AFR][1000 genomes]
rs6960458	0.85[AFR][1000 genomes]
rs705867	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7788301	0.85[AFR][1000 genomes]
rs7799441	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs858502	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs858510	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs941287	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
2	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
3	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
5	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
6	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv5867	chr7:99766774-99799755	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4299940	AP4M1	cis	Thyroid	GTEx
rs4299940	PVRIG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99775800-99798000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:99778600-99797800	Weak transcription	Fetal Intestine Small	intestine
3	chr7:99787000-99794600	Enhancers	Primary B cells from peripheral blood	blood
4	chr7:99787200-99794200	Enhancers	Primary B cells from cord blood	blood
5	chr7:99788800-99795400	Weak transcription	K562	blood
6	chr7:99790000-99808800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:99790000-99817000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:99791400-99806800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:99793200-99795200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:99793200-99796800	Weak transcription	Spleen	Spleen
11	chr7:99793200-99797800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:99793400-99795000	Weak transcription	Fetal Thymus	thymus
13	chr7:99793400-99795400	Weak transcription	Thymus	Thymus
14	chr7:99793400-99798000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:99793400-99806000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr7:99793600-99805800	Weak transcription	Primary T cells from cord blood	blood
17	chr7:99793800-99794000	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr7:99793800-99795200	Weak transcription	GM12878-XiMat	blood

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